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Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-35180-x
By:
- Gerdes, Patricia;
- Lim, Sue Mei;
- Ewing, Adam D.;
- Larcombe, Michael R.;
- Chan, Dorothy;
- Sanchez-Luque, Francisco J.;
- Walker, Lucinda;
- Carleton, Alexander L.;
- James, Cini;
- Knaupp, Anja S.;
- Carreira, Patricia E.;
- Nefzger, Christian M.;
- Lister, Ryan;
- Richardson, Sandra R.;
- Polo, Jose M.;
- Faulkner, Geoffrey J.
Publication type:
Article
Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.
Published in:
Mobile DNA, 2016, v. 7, p. 1, doi. 10.1186/s13100-016-0076-6
By:
- Carreira, Patricia E.;
- Ewing, Adam D.;
- Guibo Li;
- Schauer, Stephanie N.;
- Upton, Kyle R.;
- Fagg, Allister C.;
- Morell, Santiago;
- Kindlova, Michaela;
- Gerdes, Patricia;
- Richardson, Sandra R.;
- Bo Li;
- Gerhardt, Daniel J.;
- Jun Wang;
- Brennan, Paul M.;
- Faulkner, Geoffrey J.
Publication type:
Article
Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis.
Published in:
Mobile DNA, 2014, v. 5, n. 1, p. 1, doi. 10.1186/1759-8753-5-15
By:
- Upton, Kyle R.;
- Faulkner, Geoffrey J.
Publication type:
Article
Corrigendum: Tiny RNAs associated with transcription start sites in animals.
Published in:
2009
By:
- Taft, Ryan J;
- Glazov, Evgeny A;
- Cloonan, Nicole;
- Simons, Cas;
- Stephen, Stuart;
- Faulkner, Geoffrey J;
- Lassmann, Timo;
- Forrest, Alistair R R;
- Grimmond, Sean M;
- Schroder, Kate;
- Irvine, Katharine;
- Arakawa, Takahiro;
- Nakamura, Mari;
- Kubosaki, Atsutaka;
- Hayashida, Kengo;
- Kawazu, Chika;
- Murata, Mitsuyoshi;
- Nishiyori, Hiromi;
- Fukuda, Shiro;
- Kawai, Jun
Publication type:
Correction Notice
The regulated retrotransposon transcriptome of mammalian cells.
Published in:
Nature Genetics, 2009, v. 41, n. 5, p. 563, doi. 10.1038/ng.368
By:
- Faulkner, Geoffrey J.;
- Kimura, Yasumasa;
- Daub, Carsten O.;
- Shivangi Wani;
- Plessy, Charles;
- Irvine, Katharine M.;
- Schroder, Kate;
- Cloonan, Nicole;
- Steptoe, Anita L.;
- Lassmann, Timo;
- Waki, Kazunori;
- Hornig, Nadine;
- Arakawa, Takahiro;
- Takahashi, Hazuki;
- Kawai, Jun;
- Forrest, Alistair R. R.;
- Suzuki, Harukazu;
- Hayashizaki, Yoshihide;
- Hume, David A.;
- Orlando, Valerio
Publication type:
Article
Tiny RNAs associated with transcription start sites in animals.
Published in:
Nature Genetics, 2009, v. 41, n. 5, p. 572, doi. 10.1038/ng.312
By:
- Taft, Ryan J.;
- Glazov, Evgeny A.;
- Cloonan, Nicole;
- Simons, Cas;
- Stephen, Stuart;
- Faulkner, Geoffrey J.;
- Lassmann, Timo;
- Forrest, Alistair R. R.;
- Grimmond, Sean M.;
- Schroder, Kate;
- Irvine, Katharine;
- Arakawa, Takahiro;
- Nakamura, Mari;
- Kubosaki, Atsutaka;
- Hayashida, Kengo;
- Kawazu, Chika;
- Murata, Mitsuyoshi;
- Nishiyori, Hiromi;
- Fukuda, Shiro;
- Kawai, Jun
Publication type:
Article
Stem cell transcriptome profiling via massive-scale mRNA sequencing.
Published in:
Nature Methods, 2008, v. 5, n. 7, p. 613, doi. 10.1038/nmeth.1223
By:
- Cloonan, Nicole;
- Forrest, Alistair R. R.;
- Kolle, Gabriel;
- Gardiner, Brooke B. A.;
- Faulkner, Geoffrey J.;
- Brown, Mellissa K.;
- Taylor, Darrin F.;
- Steptoe, Anita L.;
- Wani, Shivangi;
- Bethel, Graeme;
- Robertson, Alan J.;
- Perkins, Andrew C.;
- Bruce, Stephen J.;
- Lee, Clarence C.;
- Ranade, Swati S.;
- Peckham, Heather E.;
- Manning, Jonathan M.;
- McKernan, Kevin J.;
- Grimmond, Sean M.
Publication type:
Article
Genetic control of the innate immune response.
Published in:
BMC Immunology, 2003, v. 4, p. 5, doi. 10.1186/1471-2172-4-5
By:
- Wells, Christine A.;
- Ravasi, Timothy;
- Faulkner, Geoffrey J.;
- Carninci, Piero;
- Okazaki, Yasushi;
- Hayashizaki, Yoshihide;
- Sweet, Matthew;
- Wainwright, Brandon J.;
- Hume, David A.
Publication type:
Article
The evolving gene regulatory landscape—a tinkerer of complex creatures.
Published in:
2021
By:
- Faulkner, Geoffrey J.
Publication type:
Editorial
Endogenous retroviruses in the origins and treatment of cancer.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02357-4
By:
- Jansz, Natasha;
- Faulkner, Geoffrey J.
Publication type:
Article
Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02369-0
By:
- Troskie, Robin-Lee;
- Jafrani, Yohaann;
- Mercer, Tim R.;
- Ewing, Adam D.;
- Faulkner, Geoffrey J.;
- Cheetham, Seth W.
Publication type:
Article
HCV Activates Somatic L1 Retrotransposition—A Potential Hepatocarcinogenesis Pathway.
Published in:
Cancers, 2021, v. 13, n. 20, p. 5079, doi. 10.3390/cancers13205079
By:
- Sudhindar, Praveen D.;
- Wainwright, Daniel;
- Saha, Santu;
- Howarth, Rachel;
- McCain, Misti;
- Bury, Yvonne;
- Saha, Sweta S.;
- McPherson, Stuart;
- Reeves, Helen;
- Patel, Arvind H.;
- Faulkner, Geoffrey J.;
- Lunec, John;
- Shukla, Ruchi
Publication type:
Article
Meeting report: mobile genetic elements and genome plasticity 2018.
Published in:
Mobile DNA, 2018, v. 9, n. 1, p. N.PAG, doi. 10.1186/s13100-018-0126-3
By:
- Abrams, John M.;
- Arkhipova, Irina R.;
- Belfort, Marlene;
- Boeke, Jef D.;
- Joan Curcio, M.;
- Faulkner, Geoffrey J.;
- Goodier, John L.;
- Lehmann, Ruth;
- Levin, Henry L.
Publication type:
Article
L1 retrotransposition in the soma: a field jumping ahead.
Published in:
Mobile DNA, 2018, v. 9, n. 1, p. N.PAG, doi. 10.1186/s13100-018-0128-1
By:
- Faulkner, Geoffrey J.;
- Billon, Victor
Publication type:
Article
L1 retrotransposons, cancer stem cells and oncogenesis.
Published in:
FEBS Journal, 2014, v. 281, n. 1, p. 63, doi. 10.1111/febs.12601
By:
- Carreira, Patricia E.;
- Richardson, Sandra R.;
- Faulkner, Geoffrey J.
Publication type:
Article
Transposable elements in the mammalian embryo: pioneers surviving through stealth and service.
Published in:
Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0965-5
By:
- Gerdes, Patricia;
- Richardson, Sandra R.;
- Mager, Dixie L.;
- Faulkner, Geoffrey J.
Publication type:
Article
An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden.
Published in:
Brain Pathology, 2022, v. 32, n. 3, p. 1, doi. 10.1111/bpa.13018
By:
- Rasmussen, Jay;
- Ewing, Adam D.;
- Bodea, Liviu‐Gabriel;
- Bodea, Gabriela O.;
- Gearing, Marla;
- Faulkner, Geoffrey J.
Publication type:
Article
Viral genome sequencing methods: benefits and pitfalls of current approaches.
Published in:
Biochemical Society Transactions, 2024, v. 52, n. 3, p. 1431, doi. 10.1042/BST20231322
By:
- Jansz, Natasha;
- Faulkner, Geoffrey J.
Publication type:
Article
Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation.
Published in:
British Journal of Cancer, 2023, v. 128, n. 7, p. 1236, doi. 10.1038/s41416-023-02154-9
By:
- Zadran, Bassier;
- Sudhindar, Praveen Dhondurao;
- Wainwright, Daniel;
- Bury, Yvonne;
- Luli, Saimir;
- Howarth, Rachel;
- McCain, Misti Vanette;
- Watson, Robyn;
- Huet, Hannah;
- Palinkas, Fanni;
- Palmini, Rolando Berlinguer;
- Casement, John;
- Mann, Derek A.;
- Oakley, Fiona;
- Lunec, John;
- Reeves, Helen;
- Faulkner, Geoffrey J.;
- Shukla, Ruchi
Publication type:
Article
Somatic retrotransposition alters the genetic landscape of the human brain.
Published in:
Nature, 2011, v. 479, n. 7374, p. 534, doi. 10.1038/nature10531
By:
- Baillie, J. Kenneth;
- Barnett, Mark W.;
- Upton, Kyle R.;
- Gerhardt, Daniel J.;
- Richmond, Todd A.;
- De Sapio, Fioravante;
- Brennan, Paul M.;
- Rizzu, Patrizia;
- Smith, Sarah;
- Fell, Mark;
- Talbot, Richard T.;
- Gustincich, Stefano;
- Freeman, Thomas C.;
- Mattick, John S.;
- Hume, David A.;
- Heutink, Peter;
- Carninci, Piero;
- Jeddeloh, Jeffrey A.;
- Faulkner, Geoffrey J.
Publication type:
Article
Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network.
Published in:
Scientific Reports, 2013, p. 1, doi. 10.1038/srep02962
By:
- Jian-Liang Li;
- Mazar, Joseph;
- Cuncong Zhong;
- Faulkner, Geoffrey J.;
- Govindarajan, Subramaniam S.;
- Zhan Zhang;
- Dinger, Marcel E.;
- Meredith, Gavin;
- Adams, Christopher;
- Shaojie Zhang;
- Mattick, John S.;
- Ray, Animesh;
- Perera, Ranjan J.
Publication type:
Article
Visualization and analysis of RNA-Seq assembly graphs.
Published in:
Nucleic Acids Research, 2019, v. 47, n. 14, p. 7262, doi. 10.1093/nar/gkz599
By:
- Nazarie, Fahmi W;
- Shih, Barbara;
- Angus, Tim;
- Barnett, Mark W;
- Chen, Sz-Hau;
- Summers, Kim M;
- Klein, Karsten;
- Faulkner, Geoffrey J;
- Saini, Harpreet K;
- Watson, Mick;
- Dongen, Stijn van;
- Enright, Anton J;
- Freeman, Tom C
Publication type:
Article
TET enzymes: double agents in the transposable element-host genome conflict.
Published in:
Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1124-8
By:
- Gerdes, Patricia;
- Richardson, Sandra R.;
- Faulkner, Geoffrey J.
Publication type:
Article
Retrotransposons: Mobile and mutagenic from conception to death
Published in:
FEBS Letters, 2011, v. 585, n. 11, p. 1589, doi. 10.1016/j.febslet.2011.03.061
By:
- Faulkner, Geoffrey J.
Publication type:
Article
Retrotransposon Silencing During Embryogenesis: <i>Dicer</i> Cuts in LINE.
Published in:
2013
By:
- Faulkner, Geoffrey J.
Publication type:
Opinion
Processed pseudogenes: A substrate for evolutionary innovation: Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome.
Published in:
BioEssays, 2021, v. 43, n. 11, p. 1, doi. 10.1002/bies.202100186
By:
- Troskie, Robin‐Lee;
- Faulkner, Geoffrey J.;
- Cheetham, Seth W.
Publication type:
Article
Heritable L1 Retrotransposition Events During Development: Understanding Their Origins.
Published in:
BioEssays, 2018, v. 40, n. 6, p. 1, doi. 10.1002/bies.201700189
By:
- Richardson, Sandra R.;
- Faulkner, Geoffrey J.
Publication type:
Article
Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population.
Published in:
BioEssays, 2014, v. 36, n. 5, p. 475, doi. 10.1002/bies.201300181
By:
- Richardson, Sandra R.;
- Salvador‐Palomeque, Carmen;
- Faulkner, Geoffrey J.
Publication type:
Article
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data.
Published in:
Bioinformatics, 2009, v. 25, n. 19, p. 2615, doi. 10.1093/bioinformatics/btp459
By:
- Cloonan, Nicole;
- Qinying Xu;
- Faulkner, Geoffrey J.;
- Taylor, Darrin F.;
- Tang, Dave T. P.;
- Kolle, Gabriel;
- Grimmond, Sean M.
Publication type:
Article
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.
Published in:
Bioinformatics, 2009, v. 25, n. 19, p. 2613, doi. 10.1093/bioinformatics/btp438
By:
- Hashimoto, Takehiro;
- De Hoon, Michiel J. L.;
- Grimmond, Sean M.;
- Daub, Carsten O.;
- Hayashizaki, Yoshihide;
- Faulkner, Geoffrey J.
Publication type:
Article
The Role of Transposable Elements in Health and Diseases of the Central Nervous System.
Published in:
Journal of Neuroscience, 2013, v. 33, n. 45, p. 17577, doi. 10.1523/JNEUROSCI.3369-13.2013
By:
- Reilly, Matthew T.;
- Faulkner, Geoffrey J.;
- Dubnau, Joshua;
- Ponomarev, Igor;
- Gage, Fred H.
Publication type:
Article
Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.
Published in:
PLoS Genetics, 2017, v. 13, n. 3, p. 1, doi. 10.1371/journal.pgen.1006641
By:
- Baillie, J. Kenneth;
- Arner, Erik;
- Daub, Carsten;
- De Hoon, Michiel;
- Itoh, Masayoshi;
- Kawaji, Hideya;
- Lassmann, Timo;
- Carninci, Piero;
- Forrest, Alistair R. R.;
- Hayashizaki, Yoshihide;
- null, null;
- Faulkner, Geoffrey J.;
- Wells, Christine A.;
- Rehli, Michael;
- Pavli, Paul;
- Summers, Kim M.;
- Hume, David A.
Publication type:
Article
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.
Published in:
PLoS Computational Biology, 2018, v. 14, n. 3, p. 1, doi. 10.1371/journal.pcbi.1005934
By:
- Baillie, J. Kenneth;
- Bretherick, Andrew;
- Haley, Christopher S.;
- Clohisey, Sara;
- Gray, Alan;
- Neyton, Lucile P. A.;
- Barrett, Jeffrey;
- Stahl, Eli A.;
- Tenesa, Albert;
- Andersson, Robin;
- Brown, J. Ben;
- Faulkner, Geoffrey J.;
- Lizio, Marina;
- Schaefer, Ulf;
- Daub, Carsten;
- Itoh, Masayoshi;
- Kondo, Naoto;
- Lassmann, Timo;
- Kawai, Jun;
- null, null
Publication type:
Article

Found: 33